When you are fighting alongside Alyx later in the game, at one point you will encounter a door where she tells you to go on without her, while she heads up to the communications room to unlock doors for you. Push her into the corner left of the door, then run in and watch it close behind you. As the next area is loading, she will appear next to you. This clone does not talk, and is not always there; however, later when both of you fight a group of soldiers, there are two of them.